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Issue: Vol. 5866 No. 2: 11 Aug. 2026
Type: Article
Published: 2026-08-11
DOI: 10.11646/zootaxa.5866.2.6
Page range: 305-319
Abstract views: 1826
PDF downloaded: 638

A new species of Papuan groundsnake (Squamata: Colubridae: Lielaphis) from New Guinea

Life Sciences Section; Negaunee Integrative Research Center; Field Museum of Natural History; Chicago; Illinois; USA
Museum of Natural Sciences and Department of Biological Sciences; Louisiana State University; Baton Rouge; Louisiana; USA
Slippery Rock University; College of Engineering and Science; Department of Biology; Slippery Rock; Pennsylvania; USA; Department of Mammalogy; Division of Vertebrate Zoology; American Museum of Natural History; New York; New York; USA
Papua New Guinea National Museum and Art Gallery; P.O. Box 5560; Boroko; National Capital District; Papua New Guinea
Virginia Museum of Natural History; Martinsville; Virginia; USA
Department of Biology; University of Kentucky; Lexington; Kentucky; USA
Life Sciences Section; Negaunee Integrative Research Center; Field Museum of Natural History; Chicago; Illinois; USA
Reptilia Morphology phylogenetics Serpentes systematics taxonomy

Abstract

The recently resurrected genus Lielaphis (Squamata: Colubridae) is comprised of 19 medium-sized, terrestrial snakes collectively regarded as groundsnakes. Although found primarily in New Guinea, a biologically megadiverse region with high conservation priorities, Lielaphis remain poorly studied due to their largely homogenous appearance, elusive nocturnal nature, limited records, and complex taxonomic history, leaving high potential for undescribed species still existing within this group. Using high-throughput sequence data of 12 previously described species of Lielaphis and representatives of its sister taxon, Stegonotus, we apply an integrative approach combining genetic analyses with morphological examinations using vouchered specimens to explore the cryptic diversity of Lielaphis. We place particular emphasis on populations occurring on and adjacent to mainland New Guinea. We identify both molecular and morphological evidence for a new species, Lielaphis slashi sp. nov. from the northeastern lowlands of mainland New Guinea, bringing the number of Lielaphis species to 20, along with a potential range extension of L. aplini. Despite the recent resurgence of interest in New Guinea’s snake diversity, our findings highlight persistent knowledge gaps, emphasizing the need for more comprehensive taxonomic studies of the speciose New Guinea herpetofauna.

References

  1. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D. & Pyshkin, A.V. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19 (5), 455–477. https://doi.org/10.1089/cmb.2012.0021
  2. Bernstein, J.M. & Ruane, S. (2022) Maximizing molecular data from low-quality fluid-preserved specimens in natural history collections. Frontiers in Ecology and Evolution, 10, 893088. https://doi.org/10.3389/fevo.2022.893088
  3. Bernstein, J.M., Austin, C.C., Soto-Centeno, J.A., Huang, T., Roberts, J.R., McGuire, J.A., Iskandar, D., Frederick, J.H., Weinell, J.L., Brown, R.M. & Ruane, S. (2026) Diversification and colonization in the Indo-Australian Archipelago: genomic insights from colubrid snakes. Journal of Biogeography, 53 (4), e70202. https://doi.org/10.1111/jbi.70202
  4. Bolger, A.M., Lohse, M. & Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30 (15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
  5. Boulenger, G.A. (1895) On a collection of reptiles and batrachians from Ferguson Island, D'Entrecasteaux Group, British New Guinea. The Annals and Magazine of Natural History, Series 6, 16, 28–32. https://doi.org/10.1080/00222939508680222
  6. Bruxaux, J., Gabrielli, M., Ashari, H., Prŷs-Jones, R., Joseph, L., Milá, B., Besnard, G. & Thébaud, C. (2018) Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): implications for the biogeography and conservation of New Guinean lowland birds. Molecular Phylogenetics and Evolution, 120, 248–258. https://doi.org/10.1016/j.ympev.2017.11.022
  7. Chernomor, O., von Haeseler, A. & Minh, B.Q. (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Systematic Biology, 65 (6), 997–1008. https://doi.org/10.1093/sysbio/syw037
  8. Del Fabbro, C., Scalabrin, S., Morgante, M. & Giorgi, F.M. (2013) An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One, 8 (12), e85024. https://doi.org/10.1371/journal.pone.0085024
  9. Doria, G. (1875) Enumerazione dei rettili raccolti dal Dott. O. Beccari in Amboina alle Isole Aru ed alle Isole Kei durante gli anni 1872–73. Annali del Museo Civico di Storia Naturale di Genova, 6, 325–357.
  10. Dubey, S., Brown, G.P., Madsen, T. & Shine, R. (2008) Male-biased dispersal in a tropical Australian snake (Stegonotus cucullatus, Colubridae). Molecular Ecology, 17 (15), 3506–3514. https://doi.org/10.1111/j.1365-294x.2008.03859.x
  11. Duméril, A.M.C., Bibron, G. & Duméril, A.H.A. (1854) Erpétologie générale ou Histoire naturelle complète des reptiles. Vol. 7. Partie 1. Roret, Paris, xvi + 780 pp. https://doi.org/10.5962/bhl.title.112278
  12. Earl, D.A. & vonHoldt, B.M. (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4 (2), 359–361. https://doi.org/10.1007/s12686-011-9548-7
  13. Elith, J., Graham, C.H., Anderson, R.P., Dudík, M., Ferrier, S., Guisan, A., Hijmans, R.J., Huettmann, F., Leathwick, J.R., Lehmann, A. & Li, J. (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography, 29 (2), 129–151.
  14. Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14 (8), 2611–2620. https://doi.org/10.1111/j.1365-294x.2005.02553.x
  15. Faircloth, B.C., McCormack, J.E., Crawford, N.G., Harvey, M.G., Brumfield, R.T. & Glenn, T.C. (2012) Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology, 61 (5), 717–726. https://doi.org/10.1093/sysbio/sys004
  16. Faircloth, B.C. (2013) illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. Available from: https://doi.org/10.6079/J9ILL (accessed 10 May 2025)
  17. Faircloth, B.C. (2016) PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics, 32 (5), 786–788. https://doi.org/10.1093/bioinformatics/btv646
  18. Ferreira, F., Oliver, P., Kraus, F., Günther, R., Richards, S., Tjaturadi, B., Arida, E., Hamidy, A., Riyanto, A., Trilaksono, W. & Thébaud, C. (2025) Molecular and acoustic evidence for large-scale underestimation of frog species diversity on New Guinea. Frontiers of Biogeography, 18, e137988. https://doi.org/10.21425/fob.18.137988
  19. Fick, S.E. & Hijmans, R.J. (2017) WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37 (12), 4302–4315. https://doi.org/10.1002/joc.5086
  20. Filer, C., Keenan, R.J., Allen, B.J. & McAlpine, J.R. (2009) Deforestation and forest degradation in Papua New Guinea. Annals of Forest Science, 66 (8), 813. https://doi.org/10.1051/forest/2009067
  21. Gaveau, D.L.A., Santos, L., Locatelli, B., Salim, M.A., Husnayaen, H., Meijaard, E., Heatubun, C. & Sheil, D. (2021) Forest loss in Indonesian New Guinea (2001–2019): trends, drivers and outlook. Biological Conservation, 261, 109225. https://doi.org/10.1016/j.biocon.2021.109225
  22. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59 (3), 307–321. https://doi.org/10.1093/sysbio/syq010
  23. Günther, A. (1865) Fourth account of new species of snakes in the collection of the British Museum. The Annals and Magazine of Natural History, Series 3, 15, 89–98. https://doi.org/10.1080/00222936508681770
  24. Günther, A. (1872) Seventh account of new species of snakes in the collection of the British Museum. The Annals and Magazine of Natural History, Series 4, 9, 13–37. https://doi.org/10.1080/002229372011951771
  25. Günther, A. (1883) Description of two snakes from the 'Challenger' collections. The Annals and Magazine of Natural History, Series 5, 11, 136–137. https://doi.org/10.1080/00222938309459109
  26. Hengl, T., Mendes de Jesus, J., Heuvelink, G.B.M., Ruiperez Gonzalez, M., Kilibarda, M., Blagotić, A., Shangguan, W., Wright, M.N., Geng, X., Bauer-Marschallinger, B. & Guevara, M.A. (2017) SoilGrids250m: global gridded soil information based on machine learning. PLoS One, 12 (2), e0169748. https://doi.org/10.1371/journal.pone.0169748
  27. Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q. & Vinh, L.S. (2018) UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35 (2), 518–522. https://doi.org/10.1093/molbev/msx281
  28. Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24 (11), 1403–1405. https://doi.org/10.1093/bioinformatics/btn129
  29. Jombart, T., Devillard, S. & Balloux, F. (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11 (1), 94. https://doi.org/10.1186/1471-2156-11-94
  30. Jombart, T. & Ahmed, I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics, 27 (21), 3070–3071. https://doi.org/10.1093/bioinformatics/btr521
  31. Kaiser, C.M., Kaiser, H. & O’Shea, M. (2018) The taxonomic history of Indo-Papuan groundsnakes, genus Stegonotus Duméril et al., 1854 (Colubridae), with some taxonomic revisions and the designation of a neotype for S. parvus (Meyer, 1874). Zootaxa, 4512 (1), 1–73. https://doi.org/10.11646/zootaxa.4512.1.1
  32. Kaiser, C.M., O’Shea, M. & Kaiser, H. (2019) A new species of Indo-Papuan groundsnake, genus Stegonotus Duméril et al., 1854 (Serpentes, Colubridae), from the Bird’s Head Peninsula of West Papua, Indonesia, with comments on differentiating morphological characters. Zootaxa, 4590 (2), 201–230. https://doi.org/10.11646/zootaxa.4590.2.1
  33. Kaiser, H., Kaiser, C.M., Mecke, S. & O'Shea, M. (2021) A new species of Stegonotus (Serpentes: Colubridae) from the remnant coastal forests of southern Timor-Leste. Zootaxa, 5027 (4), 489–514. https://doi.org/10.11646/zootaxa.5027.4.2
  34. Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A. & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14 (6), 587–589. https://doi.org/10.1038/nmeth.4285
  35. Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint, arXiv:1303.3997.
  36. Lindholm, W.A. (1905) Ueber einige Eidechsen und Schlangen aus Deutsch-Neuguinea. Jahrbücher des Nassauischen Vereins für Naturkunde, 58, 227–240.
  37. McDowell, S.B. (1972) The species of Stegonotus (Serpentes, Colubridae) in Papua New Guinea. Zoologische Mededelingen, 47 (2), 6–26.
  38. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. & DePristo, M.A. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20 (9), 1297–1303. https://doi.org/10.1101/gr.107524.110
  39. Merow, C., Smith, M.J. & Silander, J.A. Jr (2013) A practical guide to MaxEnt for modeling species’ distributions: what it does, and why inputs and settings matter. Ecography, 36 (10), 1058–1069. https://doi.org/10.1111/j.1600-0587.2013.07872.x
  40. Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von Haeseler, A. & Lanfear, R. (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37 (5), 1530–1534. https://doi.org/10.1093/molbev/msaa015
  41. Mittermeier, R.A., Mittermeier, C.G., Brooks, T.M., Pilgrim, J.D., Konstant, W.R., Da Fonseca, G.A.B. & Kormos, C. (2003) Wilderness and biodiversity conservation. Proceedings of the National Academy of Sciences of the United States of America, 100 (18), 10309–10313. https://doi.org/10.1073/pnas.1732458100
  42. Meyer, A.B. (1874) Eine Mittheilung von Herrn Dr. Adolf Bernhard Meyer über die von ihm auf Neu-Guinea und den Inseln Jobi, Mysore und Mafoor im Jahre 1873 gesammelten Amphibien. Monatsberichte der Königlich Preussischen Akademie der Wissenschaften zu Berlin, 1874, 128–140.
  43. Myers, N., Mittermeier, R.A., Mittermeier, C.G., Da Fonseca, G.A.B. & Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature, 403 (6772), 853–858. https://doi.org/10.1038/35002501
  44. Nelson, P.N., Gabriel, J., Filer, C., Banabas, M., Sayer, J.A., Curry, G.N., Koczberski, G. & Venter, O. (2014) Oil palm and deforestation in Papua New Guinea. Conservation Letters, 7 (3), 188–195. https://doi.org/10.1111/conl.12058
  45. Nguyen, L.T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32 (1), 268–274. https://doi.org/10.1093/molbev/msu300
  46. O’Shea, M. & Richards, S.J. (2021) A striking new species of Papuan groundsnake (Stegonotus: Colubridae) from southern Papua New Guinea, with a dichotomous key to the genus in New Guinea. Zootaxa, 4926 (1), 26–42. https://doi.org/10.11646/zootaxa.4926.1.2
  47. Oliver, L.A., Rittmeyer, E.N., Kraus, F., Richards, S.J. & Austin, C.C. (2013) Phylogeny and phylogeography of Mantophryne (Anura: Microhylidae) reveals cryptic diversity in New Guinea. Molecular Phylogenetics and Evolution, 67 (3), 600–607. https://doi.org/10.1016/j.ympev.2013.02.023
  48. Oliver, P.M., Bower, D.S., McDonald, P.J., Kraus, F., Luedtke, J., Neam, K., Hobin, L., Chauvenet, A.L.M., Allison, A., Arida, E., Clulow, S., Günther, R., Nagombi, E., Tjaturadi, B., Travers, S.L. & Richards, S.J. (2022) Melanesia holds the world’s most diverse and intact insular amphibian fauna. Communications Biology, 5 (1), 1182. https://doi.org/10.1038/s42003-022-04105-1
  49. Phillips, S.J., Anderson, R.P. & Schapire, R.E. (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190 (3–4), 231–259. https://doi.org/10.1016/j.ecolmodel.2005.03.026
  50. Phillips, S.J. & Dudík, M. (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31 (2), 161–175. https://doi.org/10.1111/j.0906-7590.2008.5203.x
  51. Polhemus, D.A. & Polhemus, J.T. (1998) Assembling New Guinea: 40 million years of island arc accretion as indicated by the distributions of aquatic Heteroptera (Insecta). In: Hall, R. & Holloway, J.D. (Eds.), Biogeography and Geological Evolution of SE Asia. Backhuys Publishers, Leiden, pp. 327–340.
  52. Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155 (2), 945–959. https://doi.org/10.1093/genetics/155.2.945
  53. Roberts, J.R. & Austin, C.C. (2020) A new species of New Guinea Worm-Eating Snake (Elapidae: Toxicocalamus Boulenger, 1896), with comments on postfrontal bone variation based on micro-computed tomography. Journal of Herpetology, 54 (4), 446–459. https://doi.org/10.1670/20-043
  54. Roberts, J.R., Iova, B. & Austin, C.C. (2022) A new species of New Guinea Worm-Eating Snake (Serpentes, Elapidae, Toxicocalamus Boulenger, 1896) from Western Highlands Province, Papua New Guinea. Zoosystematics and Evolution, 98 (2), 399–409. https://doi.org/10.3897/zse.98.90520
  55. Radosavljevic, A. & Anderson, R.P. (2014) Making better Maxent models of species distributions: complexity, overfitting and evaluation. Journal of Biogeography, 41 (4), 629–643. https://doi.org/10.1111/jbi.12227
  56. Roycroft, E., Fabre, P.H., MacDonald, A.J., Moritz, C., Moussalli, A. & Rowe, K.C. (2022) New Guinea uplift opens ecological opportunity across a continent. Current Biology, 32 (19), 4215–4224. https://doi.org/10.1016/j.cub.2022.08.021
  57. Ruane, S., Richards, S.J., McVay, J.D., Tjaturadi, B., Krey, K. & Austin, C.C. (2018) Cryptic and non-cryptic diversity in New Guinea ground snakes of the genus Stegonotus Duméril, Bibron and Duméril, 1854: a description of four new species (Squamata: Colubridae). Journal of Natural History, 52 (13–16), 917–944. https://doi.org/10.1080/00222933.2017.1391959
  58. Sabaj, M.H. (2025) Codes for Natural History Collections in Ichthyology and Herpetology (online supplement), Version 9.7 (3 Mar 2025). American Society of Ichthyologists and Herpetologists, Washington, DC. Available from: https://www.asih.org/resources/standard-symbolic-codes (accessed 15 January 2026)
  59. Schlegel, H. (1837) Essai sur la physionomie des serpens. Partie descriptive. J. Kips, J.H.Z. & W.P. van Stockum, La Haye, xvi + 606 pp. https://doi.org/10.5962/bhl.title.4273
  60. Shearman, P. & Bryan, J. (2011) A bioregional analysis of the distribution of rainforest cover, deforestation and degradation in Papua New Guinea. Austral Ecology, 36 (1), 9–24. https://doi.org/10.1111/j.1442-9993.2010.02111.x
  61. Shine, R. (1991) Strangers in a strange land: ecology of the Australian colubrid snakes. Copeia, 1991 (1), 120–131. https://doi.org/10.2307/1446254
  62. Shine, R. (1994) Sexual size dimorphism in snakes revisited. Copeia, 1994 (2), 326–346. https://doi.org/10.2307/1446982
  63. Singhal, S., Grundler, M., Colli, G. & Rabosky, D.L. (2017) Squamate conserved loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Molecular Ecology Resources, 17 (6), e12–e24. https://doi.org/10.1111/1755-0998.12681
  64. Slavenko, A., Allison, A., Austin, C.C., Bauer, A.M., Brown, R.M., Fisher, R.N., Ineich, I., Iova, B., Karin, B.R., Kraus, F., Mecke, S., Meiri, S., Morrison, C., Oliver, P.M., O’Shea, M., Richmond, J.Q., Shea, G.M., Tallowin, O.J.S. & Chapple, D.G. (2023) Skinks of Oceania, New Guinea, and Eastern Wallacea: an underexplored biodiversity hotspot. Pacific Conservation Biology, 29 (6), 526–543. https://doi.org/10.1071/pc22034
  65. Trembath, D.F., Fearn, S. & Undheim, E.A.B. (2009) Natural history of the slaty grey snake (Stegonotus cucullatus) (Serpentes: Colubridae) from tropical north Queensland, Australia. Australian Journal of Zoology, 57 (2), 119–124. https://doi.org/10.1071/zo08091
  66. Tuanmu, M.N. & Jetz, W. (2014) A global 1‐km consensus land-cover product for biodiversity and ecosystem modelling. Global Ecology and Biogeography, 23 (9), 1031–1045. https://doi.org/10.1111/geb.12182
  67. Van der Auwera, G.A., Carneiro, M.O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J. & Banks, E. (2013) From FastQ data to high-confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Current Protocols in Bioinformatics, 43 (1), 11.10.1–11.10.33. https://doi.org/10.1002/0471250953.bi1110s43
  68. Warren, D.L. & Seifert, S.N. (2011) Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria. Ecological Applications, 21 (2), 335–342. https://doi.org/10.1890/10-1171.1
  69. Werner, F. (1924) Neue oder wenig bekannte Schlangen aus dem Naturhistorischen Staatsmuseum in Wien. I. Teil. Sitzungsberichte der Akademie der Wissenschaften in Wien, Mathematisch-Naturwissenschaftliche Klasse, Abteilung I, 133, 29–56.
  70. White, T.H. Jr, Bickley, P., Brown, C., Busch, D.E., Dutson, G., Freifeld, H., Krofta, D., Lawlor, S., Polhemus, D. & Rounds, R. (2021) Quantifying threats to biodiversity and prioritizing responses: an example from Papua New Guinea. Diversity, 13 (6), 248. https://doi.org/10.3390/d13060248
  71. Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. (2018) ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19 (Supplement 6), 153. https://doi.org/10.1186/s12859-018-2129-y

How to Cite

Huang, T., Austin, C.C., Bernstein, J.M., Iova, B., Roberts, J.R., Frederick, J.H. & Ruane, S. (2026) A new species of Papuan groundsnake (Squamata: Colubridae: Lielaphis) from New Guinea. Zootaxa, 5866 (2), 305–319. https://doi.org/10.11646/zootaxa.5866.2.6